H01 visualization tools
Contents
Jupyter Notebook files
Use h01_plotly_visualizer.ipynb
notebook to generate a 2D and 3D interactive views of one or more
cells of interest from the H01 volume. Uses matplotlib and plotly
visualization methods. See an example visualization below. Note that
many cell meshes are enormous (1 GB) and may cause memory allocation
issues on typical computer systems.
plotly visualization of neurons and glia in H01 volume
Use pyvista_decimate_mesh_astro_cell_bodies_h01.ipynb
to decimate meshes (default setting is 95%) of any cell meshes that you
downloaded using the h01_plotly_visualizer.ipynb notebook.
Note that large astrocytes can take multiple hours to decimate (up to
12+ hours), whereas less complex astrocytes and neurons typically take
minutes to decimate on a typical laptop.
Use pyvista_mesh_decimation_h01_googlecolab.ipynb
to use Google Colab Pro (subscription required), if your local machine
does not have the memory or computational power to decimate large meshes
(e.g., astrocytes). A mesh requiring 12 hours on a standard machine only
took 8 minutes of processing on Google Colab Pro with High-RAM
option.
Use vtk_decimated_astro_meshes_h01.ipynb
to generate a 3D interactive render of decimated meshes using vtk and
OpenGL viewer. There are a variety of rendering methods that help bring
out more clarity of the astrocyte cell membrane, including gradient
coloring and opacity settings. Use matplotlib colormaps to change color
settings and modify the opacity levels, camera view settings, and
gradient method (linear or exponential).
